6G6R

Human Methionine Adenosyltransferase II with SAMe and PPNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A1I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729830% PEG600 0.1M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2144.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.63α = 90
b = 94β = 90
c = 116.69γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.98DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3573.298.70.0860.1060.0610.9948.558046111.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3797.10.5750.7340.4510.552.14.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5A1I1.3573.276413404798.530.138530.13730.16186RANDOM13.936
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.21-0.36-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.59
r_dihedral_angle_4_deg18.811
r_dihedral_angle_3_deg12.083
r_dihedral_angle_1_deg6.392
r_long_range_B_refined4.626
r_long_range_B_other3.868
r_scangle_other2.162
r_angle_refined_deg1.69
r_mcangle_it1.454
r_mcangle_other1.454
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.59
r_dihedral_angle_4_deg18.811
r_dihedral_angle_3_deg12.083
r_dihedral_angle_1_deg6.392
r_long_range_B_refined4.626
r_long_range_B_other3.868
r_scangle_other2.162
r_angle_refined_deg1.69
r_mcangle_it1.454
r_mcangle_other1.454
r_scbond_it1.41
r_scbond_other1.41
r_angle_other_deg1
r_mcbond_it0.931
r_mcbond_other0.931
r_chiral_restr0.111
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2942
Nucleic Acid Atoms
Solvent Atoms408
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing